1. Linked Data Initiatives at NLM
Barbara Bushman & Nancy Fallgren
Technical Services Division
National Library of Medicine
National Institutes of Health
U.S. Department of Health and Human Services
CNI Membership Meeting
December 8-9, 2014

2. Agenda Background NLM Linked Data Infrastructure Working Group
MeSH (Medical Subject Headings) RDF Pilot
Next Steps
Lessons Learned

3. Background Replace MARC format with a web-based standard
2009 Working Group on the Future of Bibliographic Control
2011 U.S. RDA Test Coordinating Committee
2012 Bibliographic Framework Initiative
2013 internal report “Linked Data at NLM: Environmental Scan, NLM Data Survey and Next Steps”
3rd party RDF versions of NLM data
RDF data published by other national libraries
RDF data published by health information organizations

4. Background Existing NLM Linked Data Initiatives PubChem RDF BIBFRAME
MESH RDF Prototype

5. NLM Linked Data Infrastructure Working Group
Broad collaboration across NLM divisions
Develop and build infrastructure for transforming, storing and publishing NLM linked data
Research best practices in publishing linked data
Recommend NLM-wide policies and guidelines for linked data publishing
Document guidance for maintaining the established linked data infrastructure
Recommend processes for future data linking projects
Prioritize NLM datasets for publication as linked data

6. NLM Linked Data WG Process
Shared working environment
SharePoint for administrative documentation
GitHub private site for development
Develop a common level of understanding
Review existing linked data initiatives
PubChem RDF
MeSH RDF prototype

7. Pilot Project: MeSH RDF
Community impact
Widely used in the health and medical community
Ability to relate many disparate health and medical resources
Community interest evidenced by
Multiple 3rd party versions published
Requests stemming from BIBFRAME experimentation
Research version of MeSH RDF already developed for internal use at NLM

8. MeSH RDF Pilot Goals
Provide authoritative MeSH RDF and ensure its maintenance and preservation
Develop an infrastructure for publishing NLM linked data
Increase our knowledge of MeSH use cases

9. Decisions URI (id.nlm.nih.gov)
Predicates (create our own vs. existing vocabularies)
License
Consultants

10. How to Provide the Linked Data
FTP
XML, XSLT, RDF
SPARQL endpoint
MeSH RDF files loaded into a graph
Stored in Virtuoso triple store
Accessible via Lodestar interface

11. Creating MeSH RDF

12. Transformation of MeSH XML to MeSH RDF
Creating MeSH RDF
Transformation of MeSH XML to MeSH RDF
USERS
NLM PUBLIC
NLM INTERNAL

14. Anti-Bacterial Agents
MeSH in RDF
meshv:D015242
meshv:D015242
meshv:Q000009
meshv:allowableQualifier
meshv:D015242
meshv:D000900
meshv:pharmacologicalAction
meshv:D000900
Anti-Bacterial Agents
label

15. Anti-Bacterial Agents
MeSH Triples Graph
Ofloxacin
label
meshv:D000900
meshv:pharmacologicalAction
Anti-Bacterial Agents
meshv:Q000009
meshv:allowableQualifier
meshv:D015242
mesh:D015242
mesh:Q000009
meshv:allowableQualifier
mesh:D015242
mesh:D000900
meshv:pharm.Action
mesh:D000900
Anti-Bacterial Agent
label

16. XML2RDF Modeling Issues
Descriptor/Qualifier pairs
Not exposed in MeSH XML
How to handle ‘illegal’ descriptor/qualifier combinations
Some XML elements only used internally
Tree nodes
Logic for hierarchical inheritance is inferred

17. MeSH Trees for Eye

18. Ontological Modeling Issues
The arrows represent broader relationships, but are eyebrows really a narrower term for sense organs?

19. Ontological Modeling Issues
Face D005145
Sense Organs
D012679
meshv:treeNumber
meshv:treeNumber A
A09
meshv:broader
meshv:broader
meshv:
broaderTransitive
meshv:
broaderTransitive
Eye
D005123 A
A09.371
meshv:treeNumber
meshv:treeNumber
meshv:
broaderTransitive
meshv:
broaderTransitive
meshv:broader
meshv:broader A A
Oculomotor
Muscles
D009801
Eyebrows
D005138
meshv:treeNumber
meshv:treeNumber

20. (Soft) Beta Launch http://id.nlm.nih.gov Work in progress
Launched Nov. 17, 2014
Work in progress
Still tweaking model and documentation
No public news announcements/press release
No links on website

21. MeSH RDF Beta Demo Landing page Technical documentation GitHub
Sample SPARQL query

27. Beta Evaluation Feedback from partners and others Public GitHub site
Customer service
Social media
Analytics
Log files

28. MeSH RDF Next Steps Next release of MeSH RDF ca. May 2015
Update to 2015 MeSH
Resolve outstanding issues raised during beta
Updating/versioning
Review MeSH XML elements

29. Using MeSH RDF at NLM Integrate with existing Linked Data Initiatives
PubChem
BIBFRAME
Future linked data projects
Research project to develop MEDLINE RDF

30. NLM Linked Data WG Next Steps
Internal report and recommendations on the future of linked data at NLM
Documentation of best practices
Recommendations on infrastructure and resources needed
Guidelines and prioritization for future projects

31. Lessons Learned Have a flexible timeframe
Collaborate broadly within your institution
Document everything
Ask for help
Understand expectations and anticipated outcomes
Create an evaluation plan
Value community collaboration

32. Questions/Comments Barbara Bushman Nancy Fallgren Beta MeSH RDF
Nancy Fallgren
Beta MeSH RDF